Non-HIV Vaccine Antigen from the Vaginal Microbiota Capable of Inducing a Mucosal Neutralizing Protective Antibody Response Against HIV Infection

ABSTRACT

A new non-HIV vaccine antigen from  Mycoplasma  sp. permease capable of inducing a mucosal neutralizing protective antibody response against HIV infection, a neutralizing antibody directed to said antigen, and a method for the identification of new antigens from the mucosal microbiota for the development of vaccines against pathogens.

The invention relates to a new non-HIV vaccine antigen from the vaginal microbiota capable of inducing a mucosal neutralizing protective antibody response against HIV infection, to a neutralizing antibody directed to said antigen, and to a method for the identification of new antigens from the mucosal microbiota for the development of vaccines against pathogens.

Despite thirty years of study, there is no HIV vaccine. HIV-exposed uninfected individuals are currently the focus of intense studies because identifying the immune correlates of reduced susceptibility to HIV may offer important clues for the development of a HIV vaccine. It was hypothesized that hypermutated neutralizing monoclonal antibodies, isolated from HIV-infected patients, came from ancestor germinal B-cell lineages, primed initially by self- or non-HIV-1 antigens and boosted for HIV Env specific response by other immunogens (Haynes et al., Nature biotechnology, 2012, 30, 423-33). Along this line, it has been recently suggested to design HIV immunogens that target specific germline B-cell receptors (BCR; Jardine et al., Science, 2013, 340, 711-6). This was achieved by the “reverse-design” of antigens from the native HIV-gp120 CD4-binding site (CD4bs-gp120) epitope to initiate the binding with germline B-cells receptors. As expected, affinity comparison of various hypermutated neutralizing monoclonal antibodies (VRC01, 12A12, 3BNC60, NIH46-45 PGV04, PGV19, PGV20, VRC-CH31) with that of their germline version shows that the affinity of the antibody precursor is 2000 to 20000 times lower for the domain CD4bs-gp120 than that of the hypermutated versions (Hoot, S. et al., PLoS pathogens, 2013, 9, e1003106). Conversely, to determine the original epitope recognized by VRC01, several successive point mutations of CD4bs-gp120 domain were needed to better fit with the germinal BCR (composed by an heavy chain encoded by unmutated hVH1-2*2). According to the authors, only rare mutation events changing the antigenic nature of gp120 during infection would generate an epitope capable of activating a population of naive B-cells, precursors of a protective antibody response. This population would not be recruited by the native form of the envelope protein. The difficulty of this approach is to trace the historical evolution of viral antigens during the infection in the patient. In addition reverse-designed HIV antigens were not shown to be capable of eliciting HIV neutralizing antibodies by active immunisation.

The transgenic mouse strain HAMIGA (EP patent 1 680 449) is a humanized transgenic mouse strain expressing human/murine chimeric IgAs with human IgA heavy chain constant regions (CH1 to CH3) and mouse heavy chain variable region and light chain variable and constant regions (VH, VL and CL).

The inventors have shown that a monoclonal IgA antibody isolated from humanized HAMIGA transgenic mice immunised with a recombinant truncated permease of Mycoplasma genitalium (fragment 431 to 875 of M. genitalium ABC transporter permease protein GenBank accession number AAC72488.1 or SEQ ID NO: 1), a potential pathogen of the genital tract, is able to neutralize HIV-1 primary isolates. This is one of the rare HIV-1 neutralizing monoclonal antibody induced by active immunisation (Nishiyama, Y. et al., The Journal of Biological Chemistry, 2009, 284, 30627-30642; Sreepian, A. et al., Journal of Immune based Therapies and Vaccines, 2009, 7, 5) and the first to be elicited by a HIV-1 independent antigen. All the others have been isolated from HIV infected patients (McCoy, L. E. & Weiss, R. A. The Journal of Experimental Medicine, 2013, 210, 209-223). The characteristics of this IgA antibody and the nature of the immunogen suggest that the natural immune response to genital microbiota (commensals and/or pathogens) may contribute to the natural resistance to HIV infection.

In view of these results, Mycoplasma genitalium permease protein (SEQ ID NO: 1) and other Mycoplasma species. (M. sp.) permeases capable of inducing antibodies cross-reacting with M. genitalium permease protein of SEQ ID NO: 1 represent promising candidates to initiate an anti-HIV vaccine protocol based on their ability to prime B-cell clones, able to further recognize native HIV-antigens.

Therefore, a first aspect of the invention relates to a Mycoplasma sp. permease antigen or a polynucleotide encoding said antigen in expressible form for use as a medicament.

The antigen of the invention which is capable of inducing a specific immune response is for use as a vaccine, in particular an anti-HIV vaccine.

In the following description, unless otherwise specified, Mycoplasma permease, M. sp. permease, M. permease or permease refers to M. genitalium permease protein (SEQ ID NO: 1) and other Mycoplasma species. permeases capable of inducing antibodies cross-reacting with M. genitalium permease protein of SEQ ID NO: 1 Mycoplasma genitalium permease is the product of the locus tag MG 468 (complement of positions 570994 to 576345 on Mycoplasma genitalium G37 genome sequence GenBank accession number L43967.2). M. genitalium permease amino acid sequence corresponds to GenBank accession number AAC72488.1 or SEQ ID NO: 1.

In the following description, the standard one letter amino acid code is used.

The Mycoplasma sp. permease antigen or permease antigen according to the invention refers to an antigen comprising a protein/peptide derived from M. sp. permease, which protein/peptide is capable of inducing anti-permease antibodies which cross-react with HIV and neutralize HIV. The antibodies induced by the permease antigen which cross-react with HIV and neutralize HIV are named hereafter as anti-permease antibodies, HIV cross-reactive and neutralizing or HIV cross-reactive and neutralizing anti-permease antibodies.

In particular, the permease antigen of the invention is capable of priming B-cell clones able to further recognize native HIV-antigens.

The invention encompasses isolated antigens derived from M. sp. permease, isolated polynucleotides encoding said antigens, as well as the natural permease antigen of Mycoplasma sp. and the natural polynucleotide of Mycoplasma sp. encoding said antigen. The isolated permease antigens include isolated, natural, recombinant and synthetic antigens comprising or consisting of Mycoplasma sp. permease protein or immunogenic derivatives thereof such as for example M. sp. permease variants, peptide fragments of said protein or variants, and modified proteins/peptides derived from said protein, variants or fragments.

M. sp. permease protein variants are derived from wild-type amino acid sequences by the introduction of one or more mutations (deletion, insertion, and/or substitution) at specific amino acid positions. M. sp. permease protein variants include natural variants resulting from M. sp. permease gene polymorphism as well as artificial variants.

The antigens derived from M. sp. permease protein are functional antigens, which means that they are capable of inducing anti-permease antibodies, HIV cross-reactive and HIV infection neutralizing.

The HIV cross-reactive and neutralizing antibodies which are induced by the permease antigen of the invention recognize related epitopes in M. sp. permease and HIV Env proteins.

The permease antigen of the invention which is capable of inducing a broadly neutralizing protective immune response against HIV infection is useful as preventive and/or therapeutic HIV vaccine.

The properties of the permease protein/peptide antigen of the invention can be readily verified by technique known to those skilled in the art such as those described in the examples of the present application.

The polynucleotide encoding the antigen in expressible form refers to a nucleic acid molecule which, upon expression in a cell or a cell-free system results in a functional antigen. According to a preferred embodiment, said permease antigen comprises or consists of a Mycoplasma. sp. permease protein, a functional variant thereof or a functional fragment of at least 5 consecutive amino acids from said permease protein or variant. In some embodiments, the permease antigen derives from M. genitalium permease protein of SEQ ID NO: 1.

Preferably, said permease antigen comprises at least:

a) a protein comprising or consisting of an amino acid sequence sequence (I) which is at least 70% identical to SEQ ID NO: 4, preferably at least 75%, 80%, 85%, 90% or 95% identical to SEQ ID NO: 4, and

b) a peptide of at least 5 consecutive amino acids from said protein in a), and

wherein said protein in a) and peptide in b) are capable of inducing HIV cross-reactive and neutralizing anti-permease antibodies.

The amino acid sequence SEQ ID NO: 4 corresponds to a truncated permease protein (residues 431 to 875 of M. genitalium permease amino acid sequence SEQ ID NO: 1) including HIV cross-reactive neutralizing epitopes from the ectodomain and C-terminal tail of HIV gp41.

The permease antigen which is capable of inducing anti-permease antibodies which cross-react with HIV and neutralize HIV comprises at least one B cell or antibody epitope from M. sp. permease which is a HIV cross-reactive and neutralizing epitope.

The permease epitope cross-reacts preferably with an HIV-Env epitope, more preferably a HIV-gp41 epitope.

The permease epitope may advantageously cross-react with a HIV-gp41 ectodomain epitope from SEQ ID NO: 2.

Alternatively, the permease epitope may advantageously cross-react with an epitope of HIV-gp41 C-terminal tail. The permease epitope may cross-react with the amino acid sequence: LVGLRIVFAVLSIVNRVRQGYSPLSFQTHLPTPRGP (SEQ ID NO: 3) from HIV-gp41 C-terminal tail (positions 699 to 734 of HIV gp41, according to the numbering system of Ratner et al., Nature, 1985, 313, 277-284), which exhibits sequence homology with M. sp. permease protein, in particular with M. genitalium permease of SEQ ID NO: 1, as demonstrated in the examples of the present application.

The permease antigen of the invention comprises one or more HIV cross-reactive and neutralizing epitope(s), wherein each epitope may be either linear or conformational. In some embodiments, the permease antigen comprises at least two identical or different HIV cross-reactive and neutralizing epitopes from M. sp. permease linked to each other directly or via a peptidic spacer arm.

The percent amino acid sequence identity is defined as the percent of amino acid residues in a Compared Sequence that are identical to the Reference Sequence after aligning the sequences and introducing gaps if necessary, to achieve the maximum sequence identity. The Percent identity is then determined according to the following formula: Percent identity=100×[1−(C/R)], wherein C is the number of differences between the Reference Sequence and the Compared sequence over the entire length of the Reference sequence, wherein (i) each amino acid in the Reference Sequence that does not have a corresponding aligned amino acid in the Compared Sequence, (ii) each gap in the Reference Sequence, and (iii) each aligned amino acid in the Reference Sequence that is different from an amino acid in the Compared Sequence constitutes a difference; and R is the number amino acids in the Reference Sequence over the length of the alignment with the Compared Sequence with any gap created in the Reference Sequence also being counted as an amino acid.

Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways known to a person of skill in the art, for instance using publicly available computer software such as BLAST (Altschul et al., J. Mol. Biol., 1990, 215, 403-). When using such software, the default parameters, e.g., for gap penalty and extension penalty, are preferably used. For amino acid sequences, the BLASTP program uses as default a word length (W) of 3 and an expectation (E) of 10.

The sequence (I) is preferably selected from the group consisting of SED ID NO: 4 and a sequence which differs from SEQ ID NO: 4 by dispersed deletions and/or insertions of one to five amino acids in said sequence, amino acid substitutions, and/or N-terminal deletion(s) of one or more amino acids in said sequence. The amino acid substitution(s) in SEQ ID NO:4 are advantageously chosen from conservative substitutions, i.e., substitutions of one amino acid with another which has similar chemical or physical properties (size, charge or polarity), which generally does not adversely affect the antigenic properties of the protein/peptide. More preferably, said conservative substitution(s) are chosen within one of the following five groups: Group 1-small aliphatic, non-polar or slightly polar residues (A, S, T, P, G); Group 2-polar, negatively charged residues and their amides (D, N, E, Q); Group 3-polar, positively charged residues (H, R, K); Group 4-large aliphatic, nonpolar residues (M, L, I, V, C); and Group 5-large, aromatic residues (F, Y, W).

The permease antigen of the invention may be a full length permease protein or an immunogenic fragment thereof. In some embodiments the permease antigen comprises or consists of a protein of less than 500 amino acids, preferably of less than 400, 300, 200, 100, 50, 40 or 30 amino acids.

Examples of preferred permease antigens comprise a protein comprising or consisting of SEQ ID NO: 4 or SEQ ID NO: 7.

The invention encompasses permease protein/peptide comprising or consisting of natural amino acids (20 gene-encoded amino acids in a L- and/or D-configuration) linked via a peptide bond as well as peptidomimetics of such protein where the amino acid(s) and/or peptide bond(s) have been replaced by functional analogues. Such functional analogues include all known amino acids other than said 20 gene-encoded amino acids. A non-limitative list of non-coded amino acids is provided in Table 1A of US 2008/0234183 which is incorporated herein by reference. The invention also encompasses modified proteins/peptides derived from the above proteins/peptides by introduction of any chemical modification into one or more amino acid residues, peptide bonds, N- and/or C-terminal ends of the protein/peptide, as long as the modified peptide/protein is functional. These modifications which are introduced into the protein/peptide by the conventional methods known to those skilled in the art, include, in a non-limiting manner: the substitution of a natural amino acid with a non-proteinogenic amino acid (D amino acid or amino acid analog); the modification of the peptide bond, in particular with a bond of the retro or retro-inverso type or a bond different from the peptide bond; the cyclization, and the addition of a chemical group to the side chain or the end(s) of the protein/peptide, in particular for coupling an agent of interest to the protein of the invention. These modifications may be used to increase its antigenicity, immunogenicity and/or bioavailability, or to label the protein/peptide. For example, the permease antigen may be conjugated to a GPI moiety for anchoring the antigen to the cell membrane and exposing said antigen at the cell-surface.

In another embodiment the permease antigen is a fusion or chimeric protein comprising an amino acid sequence fused to the N-terminal and/or C-terminal end(s) of a permease protein/peptide as defined above. The length of the chimeric protein is not critical to the invention as long as the permease antigen is functional. The permease protein/peptide is fused to one or more other protein/peptide moieties including other antigen(s), in particular HIV antigens, and/or other protein/peptide moieties which enhance B-cell activation, and/or trafficking to the lymph nodes, and/or increase the stability, bioavailability, and/or allow the purification, detection, immobilization, production in expression systems, of the permease antigen of the invention.

These moieties may be selected from: (i) a protein component of a virus-like particle for exposing the antigen of the invention at the surface of virus-like nanoparticles, (ii) a membrane anchoring moiety such as the transmembrane domain of a transmembrane protein for anchoring the antigen at the cell-surface and exposing said antigen at the cell-surface (iii) a labeling moiety such as a fluorescent protein (GFP and its derivatives, BFP and YFP), (iv) a reporter moiety such as an enzyme tag (luciferase, alkaline phosphatase, glutathione-S-transferase (GST), β-galactosidase), (v) a binding moiety such as an epitope tag (polyHis6, FLAG, HA, myc.), a DNA-binding domain, a hormone-binding domain, a poly-lysine tag for immobilization onto a support, (vi) a stabilization moiety, and (vii) a targeting moiety for addressing the chimeric protein to a specific cell type or cell compartment. In addition, the permease antigen may be separated from the peptide/protein moiety by a linker which is long enough to avoid inhibiting interactions between the permease antigen peptide and the protein/peptide moiety. The linker may also comprise a recognition site for a protease, for example, for removing affinity tags and stabilization moieties from the purified chimeric protein according to the present invention.

In some embodiments, the permease antigen consists of one permease-derived protein/peptide. In other embodiments, the permease antigen comprises several identical or different permease-derived proteins and/or peptides, directly or indirectly linked to each-other by covalent or non-covalent bounds.

The polynucleotide encoding the protein/peptide in expressible form is synthetic or recombinant DNA, RNA or combination thereof, either single- and/or double-stranded. Preferably the polynucleotide comprises a coding sequence which is optimized for the host in which the protein/peptide is expressed.

In another preferred embodiment, the polynucleotide comprises or consists of SEQ ID NO: 5 or 6.

In another preferred embodiment, the polynucleotide is inserted in a vector. Preferably, said recombinant vector is an expression vector capable of expressing said polynucleotide when transfected or transformed into a host cell such as a prokaryotic or eukaryotic cell. The polynucleotide is inserted into the expression vector in proper orientation and correct reading frame for expression. Preferably, the polynucleotide is operably linked to at least one transcriptional regulatory sequence and, optionally to at least one translational regulatory sequence. Recombinant vectors include usual vectors used in genetic engineering, vaccines and gene therapy including for example plasmids and viral vectors.

Another aspect of the present invention relates to an immunogenic or vaccine composition, comprising at least the permease antigen or the polynucleotide encoding said antigen, and a pharmaceutically acceptable vehicle, and optionally, at least one pharmaceutically acceptable carrier and/or adjuvant.

The immunogenic or vaccine composition according to the invention is capable of inducing a functional mucosal protective immune response against HIV infection which can be measured by various assays which are known to those skilled in the art. Examples of such assays include with no limitation: HIV virus capture assays, Antibody-Dependent-Cellular-Cytotoxicity (ADCC) assays using primary CD89+-polynuclear effector cells, Fc-mediated inhibition assays on macrophages, macrophage phagocytosis induction assays, viral replication inhibition assays, HIV infection neutralizing assays, virus aggregation assays and transcytosis inhibition assays.

In some embodiments, the pen lease antigen is an isolated antigen. In other embodiments the permease antigen comprises whole-cell live, attenuated or inactivated Mycoplasma sp. Preferably, the permease antigen comprises live, attenuated or inactivated M. genitalium.

The polynucleotide encoding said antigen is preferably inserted in an expression vector.

The composition comprises a therapeutically effective dose of the antigen/polynucleotide/vector, e.g., sufficient to induce a specific protective immune response against HIV, in the individual to whom it is administered. The effective dose is determined and adjusted depending on factors such as the composition used, the route of administration, the physical characteristics of the individual under consideration such as sex, age and weight, concurrent medication, and other factors, that those skilled in the medical arts will recognize.

The composition is generally administered according to known procedures used for vaccination, at dosages and for periods of time effective to induce a specific protective immune response against HIV. The administration may be by injection or by oral, sublingual, intranasal, rectal or vaginal administration, inhalation, or transdermal application. Preferably, the administration is by intradermal injection or intranasal, intravaginal or intrarectal administration.

The pharmaceutical vehicles are those appropriate to the planned route of administration, which are well known in the art.

The carrier may advantageously be selected from the group consisting of: uni- or multi-lamellar liposomes, ISCOMS, virosomes, viral pseudo-particules, saponin micelles, saccharid (poly(lactide-co-glycolide)) or gold microspheres, and nanoparticules. Preferably, the composition comprises liposomes.

The adjuvant may advantageously be selected from the group consisting of: polyI:C (polyinosine-polycytidylic acid), oil emulsion, mineral substances, bacterial extracts, CpG-containing oligonucleotide, saponin, alumina hydroxide, monophosphoryl-lipid A (MPLA, a TLR4 agonist) and squalene. Preferably, the adjuvant is capable of inducing an IgA antibody response, such as for example, polyI:C (polyinosine-polycytidylic acid) adjuvant. More preferred adjuvants include polyI:C and MPLA. The composition is formulated for administration by a number of routes. Preferably, the composition is formulated for intradermal injection or local application, more preferably for intradermal, intranasal, intravaginal, or intrarectal administration. For example, the composition is formulated in a gel for local application.

According to a preferred embodiment, said composition further comprises an antibody directed to said permease antigen; the antibody forms an antigen-antibody complex with the antigen which has the advantage of increasing the immunogenicity of the antigen. Preferably, the antibody is an IgA, more preferably a human or humanized IgA. The antibody is advantageously a monoclonal antibody. For example, the antibody is a human chimeric IgA, such as the human chimeric IgA monoclonal antibody C3G4 comprising a murine IgVH segment of SEQ ID NO: 8, a murine IgVL segment of SEQ ID NO: 9, a human Ig-alpha1 constant segment of SEQ ID NO: 10 and a murine Ig-kappa constant segment of SEQ ID NO: 11, which is disclosed in the examples of the present application.

A preferred vaccine composition comprises a M. genitalium permease antigen formulated in liposomes containing monophosphoryl lipid A (MPLA). Both liposomes and MPLA contribute as adjuvant. One mL of liposomal suspension may contain 1 mg of M. genitalium permease antigen and 0.800 mg of MPLA. The vaccine composition may be formulated as a gel, for local route administration, for example nasal or vaginal route. The gel may comprise 4% w/w Natrosol® 250 HHX (Hydroxyethyl cellulose) and 1.1% w/w Benzyl alcohol, in PBS.

Another aspect of the present invention relates to a permease antigen or a polynucleotide encoding said antigen as defined above, as a prophylactic and/or therapeutic vaccine, for use in the prevention and/or treatment of HIV infection.

The invention provides also a method of vaccination against HIV infection, comprising: administering to an individual a therapeutically effective amount of the permease antigen, polynucleotide and/or vector as described above, preferably included in an immunogenic or vaccine composition as described above.

The administration of the permease antigen is used to prime B-cell clones, able to further recognize native HIV-antigens. Following, the initial priming, the anti-HIV immune response may be boosted by administration of HIV antigen(s), in particular HIV-Env antigen(s). A mixture of different HIV antigens may be used. Preferred HIV antigens are HIV gp41 ectodomain and/or C-terminal tail antigens.

The vaccination protocol may comprise an initial priming with the permease antigen comprising three administrations of permease antigen at one month interval and a final boost with HIV-1 antigen(s), one month after the last administration of permease antigen.

Another aspect of the invention relates to a combined preparation containing a permease antigen, polynucleotide, vector as described herein and HIV antigen(s), in particular HIV-Env antigen(s), for the simultaneous, separate or sequential use in the prevention and/or treatment of HIV infection.

In a preferred embodiment, said HIV infection is HIV-1 infection.

Another aspect of the invention relates to an isolated anti-permease antibody which is HIV cross-reactive and neutralizing, or a functional fragment of said antibody comprising at least the antibody binding site. Preferably, the antibody is an IgA, more preferably a human or humanized IgA, such as a human chimeric IgA. The antibody is advantageously a monoclonal antibody. In a preferred embodiment, the antibody is human chimeric IgA monoclonal antibody produced by immunisation of an HAMIGA transgenic mouse (EP patent 1 680 449) with a permease antigen as described above. For example, the antibody is the human chimeric IgA monoclonal antibody C3G4 comprising a murine IgVH segment of SEQ ID NO: 8, a murine IgVL segment of SEQ ID NO: 9, a human Ig-alpha1 constant segment of SEQ ID NO: 10 and a murine Ig-kappa constant segment of SEQ ID NO: 11, which is disclosed in the examples of the present application.

Another aspect of the invention relates to an isolated polynucleotide encoding said HIV cross-reactive and neutralizing anti-permease antibody or functional fragment thereof. In a preferred embodiment, the polynucleotide comprises the sequence SEQ ID NO: 12 or 13 which encodes the IgVH segment of SEQ ID NO: 8 and the IgVL segment of SEQ ID NO: 9, respectively.

The anti-permease antibody is a useful component of the immunogenic or vaccine composition as described above, it is also a companion diagnostic tool to evaluate the protective immune status evolution and maturation of patients treated or immunized against HIV infection, a predictive marker of resistance to HIV infection and a tool for designing HIV immunogens capable of inducing a protective neutralizing antibody response against HIV infection.

Further aspect of the present invention concerns a method for the identification of a new vaccine candidate antigen against a pathogen of interest, comprising:

a) identifying an antigen in the mucosal microbiota of an individual naturally resistant to said pathogen, preferably a human individual, wherein the microbiotal antigen is from a microorganism different from said pathogen,

b) generating an antibody against said microbiotal antigen in a),

c) assaying the neutralizing activity of the antibody obtained in b) against said pathogen, wherein a neutralizing activity of the antibody against said pathogen indicates that the microbiotal antigen is a new vaccine candidate antigen against said pathogen, for an individual which is susceptible to said pathogen.

The natural microbiota may be from the vaginal, naso-pharyngeal, lung or gastro-intestinal mucosa.

The pathogen is a microorganism which may be pathogenic in some individuals but not pathogenic in other individuals which differ from the first ones by some factors such as for example age, sex, medical history, immune status and microbiota.

According to a preferred embodiment, the pathogen is a virus.

In some embodiments of said method, said pathogen is HIV and/or said microbiota is from the vaginal mucosa. The antibody is advantageously generated by immunization of an HAMIGA transgenic mouse (EP patent 1 680 449) with the microbiotal antigen, to produce human chimeric IgAs directed against said antigen.

A neutralizing activity is indicative that the microbiotal antigen is capable of inducing a protective immune response against said pathogen. The neutralization activity may be related to an antibody which recognizes epitopes which may not be identified by standard binding assays.

Another aspect of the invention is a M. sp. permease antigen derived from M. genitalium as defined above, said permease antigen being different from M. sp. protein. Preferably, said M. sp. permease antigen is a M. genitalium permease antigen, more preferably SEQ ID NO: 4 or 7. The invention encompasses also a modified protein/peptide and a chimeric protein derived from said M. sp. permease antigen, preferably from a M. genitalium permease antigen. The invention further includes a polynucleotide encoding said M. sp. permease antigen, preferably a M. genitalium permease antigen, in particular the polynucleotide of SEQ ID NO: 5 or 6, and a vector comprising said polynucleotide.

The polynucleotide for use according to the invention is prepared by the conventional methods known in the art. For example, it is produced by amplification of a nucleic sequence by PCR or RT-PCR, by screening genomic DNA libraries by hybridization with a homologous probe, or else by total or partial chemical synthesis. The recombinant vectors are constructed and introduced into host cells by the conventional recombinant DNA and genetic engineering techniques, which are known in the art.

The protein/peptide for use according to the invention is prepared by the conventional techniques known to those skilled in the art, in particular by expression of a recombinant DNA in a suitable cell system (eukaryotic or prokaryotic) or by solid-phase or liquid-phase synthesis. More specifically, the protein and its derivatives are usually produced from the corresponding cDNA, obtained by any means known to those skilled in the art; the cDNA is cloned into an eukaryotic or prokaryotic expression vector and the protein produced in the cells modified with the recombinant vector is purified by any suitable means, in particular by affinity chromatography. The peptide and its derivatives are usually solid-phase synthesized, according to the Fmoc technique, originally described by Merrifield et al. (J. Am. Chem. Soc., 1964, 85: 2149-) and purified by reverse-phase high performance liquid chromatography.

The practice of the present invention will employ, unless otherwise indicated, conventional techniques which are within the skill of the art. Such techniques are explained fully in the literature. In addition to the above arrangements, the invention also comprises other arrangements, which will emerge from the description which follows, which refers to exemplary embodiments of the subject of the present invention, with reference to the attached drawings in which:

FIG. 1 illustrates HIV-1 infection neutralization potency (IC90) in PBMC-based neutralizing assay of purified seric IgA from HAMIGA mice immunized with Mycoplasma genitalium permease antigen (PERM) or HIV gp41-ectodomain polypeptide (GP). HAMIGA mice (10 mice per group) were immunized via two different routes (vaginal route (VAG) or intradermal route (ID)) and with two different antigens, a recombinant truncated permease antigen from M. genitalium (PERM) or the HIV gp41-ectodomain polypeptide (GP). Control HAMIGA mice (5 mice per group) were immunized with Bovine Serum Albumin (BSA) by the ID route. Seric IgA were collected and purified by affinity chromatography. Neutralizing activity of seric IgA from each immunized mouse was measured against SF162 virus strain in a PBMC based-neutralizing assay. The neutralizing activity is expressed as IC90 (Inhibitory concentration 90%), i.e., the concentration (μg/mL) of purified seric IgA that caused a 90% reduction of HIV virus infection. Only seric IgAs from permease immunized mice were able to exhibit an IC90 potency of HIV-1 infection neutralization at the range of 60 μg/mL. Despite a strong anti-gp41 binding, none of the seric IgAs from gp41-ectodomain polypeptide immunized mice was able to generate an IC90 neutralizing immune response.

FIG. 2 shows cross-reactivity by ELISA of anti-Mycoplasma genitalium permease polyclonal seric and secretory IgA antibodies with HIV gp41. HAMIGA transgenic mice were immunized with Mycoplasma genitalium (M.g.) permease antigen (P) or gp41-ectodomain polypeptide (GP) by the intradermal (ID) or intra-vaginal (VAG) routes. Anti HIV-1 gp41 and anti-M.g. permease specific polyclonal IgA antibodies were analysed by ELISA in serum and vaginal secretions of Pre-immune mice (Pre-I) and immunized mice. Although polyclonal IgA (seric and vaginal) from gp41-immunized HAMIGA mice do not show a significant binding on the permease in ELISA, polyclonal IgA from M. genitalium permease-immunized HAMIGA mice exhibit a significant cross-reactivity against gp41 ectodomain antigen.

FIG. 3 represents Coomassie-blue-stained SDS-PAGE analysis of HIV-1 neutralizing human/murine chimeric monoclonal IgA1_(κ) antibody C3G4. C3G4 was purified by affinity-chromatography and monomeric and polymeric forms of IgA were separated by size-exclusion chromatography. C3G4 contains the two forms—monomeric and polymeric—of a monoclonal IgA1. L: molecular weight marker. 1. Total fraction of mAb C3G4. 2. Monomeric-IgA enriched fraction of mAb C3G4. 3. Polymeric-IgA enriched fraction of mAb C3G4.

FIG. 4 illustrates the binding and neutralizing activity of C3G4 monoclonal anti-M. genitalium permease IgA1. A. The binding of total IgA, monomeric IgA-enriched and polymeric IgA-enriched fractions of C3G4 to M. genitalium permease was analysed by ELISA using truncated M. genitalium permease as antigen. B. The binding of total IgA, monomeric IgA-enriched and polymeric IgA-enriched fractions of C3G4 to HIV gp41 was analysed by ELISA using HIV gp41-ectodomain polypeptide as antigen. C. Neutralizing activity of monomeric IgA and polymeric IgA enriched fractions of C3G4 was measured against HIV-1/SF162 and HIV-1/QHO virus strains in a PBMC based-neutralizing assay. The neutralizing activity is expressed as IC70 (Inhibitory concentration 70%) and IC90 (Inhibitory concentration 90%), i.e., the concentration (mg/mL) of monomeric enriched or polymeric enriched fraction of C3G4 that caused a 70% and 90% reduction of HIV virus infection, respectively.

FIG. 5 illustrates the neutralization activity of C3G4 monoclonal anti-M. genitalium permease IgA1 in PBMC-based neutralizing assay on nine HIV-1 strains. Neutralizing activity of purified C3G4 polymeric IgA1 was tested on different HIV-1 laboratory and primary strains. Purified C3G4 polymeric IgA1 exhibited a neutralization activity on nine different HIV-1 strains with an IC80<18 μg/mL against HIV-1_(SF162), HIV-1_(92BR025) and HIV-1_(TV1) isolates, an IC50<1.8 μg/mL against HIV-1_(QHO) and HIV-1_(DU174) isolates and an IC50<18 μg/mL against HIV-1K_(ON), HIV-1_(92UG024), HIV-1_(89.6) and HIV-1_(RW) isolates.

FIG. 6 represents the alignment of IgH variable segments of HIV neutralizing human mAb VRC01 (SEQ ID NO: 17) directed to CD4bs-gp120 and its human unmutated ancestor IgVH1-2*2 (SEQ ID NO: 18); HIV-1 neutralizing human/murine chimeric monoclonal IgA1_(κ) antibody C3G4 (SEQ ID NO: 19) and its murine unmutated ancestor IgVH5-12 (SEQ ID NO: 20).

EXAMPLE 1 Identification of the Vaginal Immune Response in Uninfected Women Highly Exposed to HIV 1. Material and Methods 1.1 Cohorts

A cohort of 32 HIV highly-exposed uninfected women (HEUW) from sero-discordant couples was investigated in collaboration with the GHESKIO Centers (Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections) in Haiti. The control cohort included 15 HIV non-exposed uninfected subjects. None of the subjects had CCR5-Delta 32 homozygous genotype and two were heterozygous, one in HEUW group, the other in control group. The study was approved by ethical committee and informed consent was obtained from all women prior sampling.

1.2 ELISA on Vaginal Secretions

Vaginal secretions of HEUW and controls were assayed for HIV gp41-specific IgG1 and IgA antibody responses by ELISA, as previously described (Hocini et al., AIDS Res. Hum. Retroviruses, 1997, 13, 1179-).

1.3 Western-Blot on Vaginal Secretions

Vaginal secretions of HEUW and controls were assayed for HIV gp160, gp110, gp41, p68, p55, p53, p40, p34 and p25 specific IgG1 and IgA antibodies by Western-Blot as previously described (Hocini et al., AIDS Res. Hum. Retroviruses, 1997, 13, 1179-).

1.4 Inhibition of Transcytosis Assay

Inhibition of transcytosis of assay was performed as previously described (Bélec, L. et al. The Journal of infectious diseases, 2001, 184, 1412-1422).

1.5 Cloning of Mucosal Cells IgG1 and IgA Variable Regions into Phagemid Vector

Separate libraries of IgA and IgG1 Fab fragments were constructed. Briefly, messenger RNAs extracted from mucosal cells of two selected subjects were used for separate amplification of IgG1 and IgA variable regions. PCR primers corresponding to the 5′ end of all VH and VL variable domain families were combined individually with a primer derived from IgG1 or IgA first constant domain (Persson et al., Proc. Natl. Acad. Sci. USA., 1991, 88, 2432-6). The amplified DNA fragments corresponding to heavy and light chains were then cloned into a phagemid vector (Persson et al., Proc. Natl. Acad. Sci. USA., 1991, 88, 2432-6), allowing the surface display of Fab fragment (Barbas et al., Proc. Natl. Acad. Sci. USA, 1991, 88, 7978-82).

1.6 Sequencing of Recombinant IgG and IgA Fab

Individual clones, from both IgG1 and IgA libraries were sequenced using the standard Sanger dideoxy technique.

1.7 Expression of Recombinant IgG1 and IgA Fab Fragments

Recombinant Fab fragments were expressed using both E. coli (Studier and Moffat, J. Mol. Biol., 1986, 189, 113-130) and Cell-free translation (Ryabova et al., Methods Mol. Biol. 1998, 77, 179-93).

1.8 Analysis of VH Mutations

VH mutations of recombinant IgG1 and IgA were analysed as described in Wang et al., BMC bioinformatics, 2008, 9 Suppl 12, S20.

1.9 Identification of Antibody Epitope by Phage Displayed Random Peptide Libraries Screening

In order to identify the epitope recognized by the antibody, the recombinant antibody Fab fragment was screened against commercial phage displayed random peptide libraries (Ph.D. -12™ Phage Display Peptide Library Kit, NEW ENGLAND BIOLABS), according to the manufacturer's instructions. Typically, 4 to 5 rounds of selection (bio-panning) were applied.

1.10 Statistical Analysis

A Yates' chi-squared test was used to analyze the samples from Table I. The difference between control group and HIV-highly exposed group is statistically significant as long asp value<0.05.

2. Results

The immune response in the genital tract of a cohort of HIV highly exposed uninfected women (HEUW) from sero-discordant couples was investigated in collaboration with the GHESKIO Centers (Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections) in Haiti. Vaginal fluids from 32 individuals were analyzed by ELISA and Western Blot, and compared with 15 control HIV non-exposed uninfected subjects. None of the subjects had CCR5-Delta 32 homozygous genotype and two were heterozygous, one in HEUW group, the other in control group. Vaginal secretions were tested for specific IgG1 and IgA antibody responses against gp41 in ELISA. ELISA results were confirmed by western blot. Only samples showing a strong positivity with both techniques were retained for further investigation and antibody library construction.

Although all subjects were seronegative for HIV infection, 53% of the HEUW were positive in vaginal secretions for anti-gp41 IgA versus only 13% in the control group (p<0.02) whereas no significant difference was observed for anti-gp41 IgG responses (Table I).

TABLE I HIV-1 specific immune response in vaginal secretions of HEUW by WB and ELISA Positives in Positives in Control HIV highly exposed P Antibody group (n = 15) group (n = 32) value IgA WB/gp160 0 (0%)  3 (10%) NS IgA WB/gp110 0 (0%) 1 (3%) NS IgA WB/p68 0 (0%) 1 (3%) NS IgA WB/p55 0 (0%) 2 (6%) NS IgA WB/p53 0 (0%) 1 (3%) NS IgA WB/gp41  2 (13%) 17 (53%) 0.02 IgA WB/p40 0 (0%) 1 (3%) NS IgA WB/p34 0 (0%)  4 (12%) NS IgA WBP/p25 1 (6%) 2 (6%) NS IgA ELISA/gp41  3 (20%)  9 (28%) NS IgG1 WB/gp160 0  5 (16%) 0.16 IgG1 WB/gp110 0 2 (6%) NS IgG1 WB/p68 0 1 (3%) NS IgG1 WB/p55  2 (13%)  3 (10%) NS IgG1 WB/p53 0  4 (12%) NS IgG1 WB/gp41 2  8 (25%) NS IgG1 WB/p40 0 2 (6%) NS IgG1 WB/p34 0 1 (3%) NS IgG1 WB/p25 0  4 (12%) NS IgG1 ELISA gp41  2 (13%)  7 (22%) NS WB: Western blot; NS: non-significant

The functional activity of the secretions was tested by inhibition of transcytosis of HIV_(JRCSF). None of the secretions were positive in transcytosis functional assays, compared with the broad HIV-1 neutralizing monoclonal antibody 2F5 used as positive control. Therefore the transcytosis test was not further used for screening of samples.

To characterize the antibody response, mucosal cells were collected with a cytobrush from two CCR5 wild type subjects selected on the basis of their strong response against gp41 in ELISA and Western Blot and of long term unprotected sexual relationship with at least one HIV-1 seropositive partner. In order to avoid amplifying genes from the partner, all samples positive for the Prostate Specific Antigen (>50 ng/mL PSA) were discarded.

After specific amplification, IgG and IgA variable regions were cloned into a phagemid vector allowing the expression of Fab fragments at the surface of filamentous phages. In a first strategy, phages displaying a Fab binding to a recombinant gp41 antigen would have been selected. This screening step was found to be unnecessary due to the observed strongly oligoclonal profile of the cloned repertoire. In a standard situation, the analysis by sequencing of clones randomly picked from the library should give a whole set of different sequences. However, in the case of the selected subjects, the vast majority of clones was identical or very closely similar and represented a large percentage of the total population (up to 75% for VH chains). This was not due to a bias in amplification or cloning since the same result was obtained when independent libraries were constructed. The same was true for both the IgG1 and IgA libraries. To further characterize this oligoclonal mucosal repertoire, Fab fragments corresponding to the most represented antibodies were expressed as recombinant proteins.

IgG1 (called Toussaint) in association with 2 different light chains, IgA (called Makandal) in association with 2 different light chains, IgG1 (Jacmel) and IgA (Mangue). The most represented light chains were from κ1 and λ4 families. These two light chains were systematically associated with all the heavy chains since the original VH/VL chain pairing was not possible to determine. Analysis of the VH mutations showed that Makandal had a germinal un-mutated profile. In order to identify the recognized epitope, this antibody was screened against commercial phage displayed random peptide libraries. In two independent screenings, two overlapping peptides allowed for the identification of an epitope corresponding to a region in the C-terminal part of gp41: LVGLRIVFAVLSIVNRVRQGYSPLSFQTHLPTPRGP (SEQ ID NO: 3).

It was hypothesized that the mucosal oligoclonal immune response of these women might be responsible for their resistance to HIV infection and that these antibodies were induced in response to a particular microbiota and by cross-reaction with the gp41 domain of HIV envelope, could prevent the viral fusion. In order to see if the sequence of amino acids recognized by Makandal Fab had any homologies with other proteins of the environment, this sequence was compared with a protein sequence databases excluding HIV proteins. Data showed very weak matches, but interestingly, there were consistent matches with bacterial protein sequences. Among these, a permease from Mycoplasma genitalium (GenBank accession number AAC72488.1 or SEQ ID NO: 1) was selected.

EXAMPLE 2 The Permease Antigen of M. genitalium is Capable of Inducing a Systemic and a Mucosal Neutralizing Protective Antibody Response Against HIV Infection in HAMIGA Mice 1. Material and Methods 1.1 Antigens

Recombinant Truncated Permease from M. Genitalium (rPermease or PERM)

Recombinant truncated permease cDNA (SEQ ID NO: 6) prepared by gene synthesis (GeneART) was inserted in a procaryotic expression vector (pSP401, derived from pET28 cer (NOVAGEN); Peubez et al., Microbial Cell factories, 2010, 9, 65-) and expressed in E. coli BL21 strain. Tagged by a Histidine tail, the antigen (SEQ ID NO: 7) was purified by affinity chromatography on His-IMAC (BIORAD) column. The purified recombinant permease protein fragment ([rPermease]=1 mg/mL in Tris 25 mM, Arginine 0.5 M, Sucrose 5% buffer, pH 8) had a purity of 82%.

HIV Gp41 Ectodomain Peptide (GP)

Recombinant HIV-gp41 ectodomain peptide (GP) preparation is disclosed in Krell et al., European Journal of Biochemistry, 2004, 271, 1566-1579. Briefly, a 0.6 kb DNA fragment containing the sequence encoding the ectodomain of gp41 of HIV isolate LAI (amino acid sequence SEQ ID NO: 2, corresponding to amino acid residues 540 to 673 of gp160 (SEQ ID NO: 14)), was obtained by PCR amplification using, as template, a plasmid containing the gp120 sequence and the gp41 sequence of the LAI isolate. The start codon in the forward primer is a naturally occurring methionine residue. A stop codon and the DNA sequence encoding the extension GGGGSHHHHHH (SEQ ID NO: 15) were added to the reverse primer. Platinum HF polymerase (GIBCO INVITROGEN) was used, according to the manufacturer's instructions, for PCR amplification. The PCR amplified fragment was cloned directly into the vector pM1800 using the restriction sites NcoI and XhoI. The expression vector pM1800 is a derivate of pET28c (NOVAGEN, in which the F1 origin of replication has been deleted and replaced with the Cer fragment, allowing for multimer resolution. For protein expression, E. coli BL21(DE3) was transformed with the corresponding plasmids. Tagged by an Histidine tail, the ectodomain antigen (SEQ ID NO: 16) was purified by affinity chromatography on onto a 5 ml Hi-Trap Chelating column (AMERSHAM PHARMACIA BIOTECH). Protein elution was achieved using a buffer comprising 50 mMTris/HCl, 8 M urea, 500 mM NaCl and 500 mM imidazole, pH 8.0. Protein refolding was achieved by dialysis with 50 mM formate, pH 2.8. Protein was then sterile filtered and stored at −45° C.

1.2 Immunization

Immunization was performed in HAMIGA transgenic mice (EP Patent 1 680 449), a transgenic mouse strain producing human/mouse chimeric IgAs with human IgA heavy chain constant regions and mouse light chain constant regions and (heavy and light chain) variable regions. Estrous cycles of HAMIGA transgenic mice were synchronized by treatment with Depoprovera (5 days before the first immunization, 8 days- and 16 days post-immunization-2 mg/mouse/injection by subcutaneous route). HAMIGA transgenic mice (10 mice per group) were immunized by intradermal (Group ID in ear) or intravaginal (Group VAG) routes twice at two weeks of interval with the recombinant truncated permease of M. genitalium (PERM) in polyI:C adjuvant (10 μg/mouse/injection, ratio 1:2.5 PolyI:C (25 μg/mouse/injection, INVIVOGEN)). For comparison, ten HAMIGA mice were immunized with gp41-ectodomain polypeptide via the ID route (GP/ID, 10 μg/mouse/injection, in polyI:C adjuvant (10 μg/mouse/administration, ratio 1:2.5 PolyIC (25 μg/mouse/injection, INVIVOGEN)) and via the vaginal route (GP/VAG, 10 μg/mouse/administration, in polyI:C adjuvant (10 μg/mouse/administration, ratio 1:2.5 PolyIC (25μg/mouse/administration, INVIVOGEN)). As a negative control, five HAMIGA mice were immunized with Bovine Serum Albumin (BSA) antigen by ID route.

1.3 Vaginal Washes Harvest

Vaginal cavities of immunized mice were washed each day during a complete estrous cycle (4 days), by gently flushing vaginal cavity with 200 μL of physiological media (NaCl 0.9%, URGO).

1.4 Seric IgA and Secretory IgA Concentration Titration by ELISA

Seric IgA from immunized HAMIGA mice (purified by affinity chromatography) and secretory IgA prepared from vaginal washes were titered by ELISA. Briefly, 96-well plates (Maxisorp®, NUNC) were coated with 1 μg/mL of goat anti-human IgA (BECKMAN COULTER) in PBS buffer overnight at 4° C. Plates were saturated with a BSA 2%/PBS1× buffer during 30 minutes at 37° C. Incubation of the samples (secretory IgA, diluted 10 times in BSA 0.2%/PBS or purified seric IgA, diluted 100 times in BSA 0.2%/PBS) was performed at 37° C. during 2 h. Human IgA reference range (from [control hIgA]=0.2 mg/ml to 1.56 ng/mL) was incubated following the same protocol and revealed by an Alkaline-Phosphatase (AP) labelled-goat anti-hIgA polyclonal antibody (BECKMAN COULTER; diluted 2000 times in BSA 0.2%/BSA).

1.5 Preparation of Monoclonal IgA

To isolate monoclonal IgA from permease-immunised mice, immortalization of specific B-cell lymphocytes were performed, according to Kölher and Milstein protocol (Köhler, G. & Milstein, C. European Journal of Immunology, 1976, 6, 511-9). Briefly, splenocytes from permease-immunized mice were fused with mice myeloma cells (X63 Sp2/0) and subcloned on 96-wells plates. The supernatants of hybridoma clones were harvested after three weeks of culture and tested for their neutralizing activity on in vitro HIV infection inhibition assay. Each clone was cryopreserved in DMSO 10%/SVF 20%/DMEM media in liquid nitrogen.

1.6 IgA Purcation

IgA were purified by affinity chromatography. The monomeric and polymeric forms of IgA were separated by size exclusion column chromatography.

1.7 Antigen Specificity Analysis

Permease fragment/gp41-ectodomain specific IgA were assessed by ELISA using Maxisorp® 96-wells plates (NUNC) coated with 1 to 5 μg/mL of antigens overnight at 4° C. Crude supernatants, unpurified IgA from vaginal washes or purified serum IgA (diluted in PBS/Gelatin 0.2%) were incubated 2 hours at 37° C. Specific IgA binding was revealed with an AP-conjugated goat anti-human IgA antibody (1/2000 diluted, BECKMAN COULTER).

1.8 Cell Preparation

Blood samples were collected from anonymous healthy donors (Etablissement Français du Sang, EFS). Peripheral Blood Mononuclear cells were obtained by Ficoll-Hypaque sedimentation of Buffy coats. PBMCs were activated with phytohemagglutinin-A (PHA, 1 mg/mL, SIGMA) in RPMI medium-10% fetal calf serum (FCS) supplemented with antibiotics (Penicillin and Streptomycin, 100 Units/mL and 100 μg/mL, respectively) at the concentration of 10.10⁶ cells/mL for 30 minutes. Cells were then cultivated in RPMI medium-10% FCS supplemented with antibiotics at 2.10⁶ cells/mL. After 3 days, cells were frozen. PBMCs from 5 donors were thawed, pooled and culture for one day before being used in the neutralization assay.

TZM-Bl cell line was obtained through the NIH reagent program. TZM-Bl cells were cultured in RPMI medium-10% FCS supplemented with antibiotics (Penicillin and Streptomycin, 100 Units/mL and 100 μg/mL, respectively).

1.9. Virus Preparation

Primary HIV-1 isolates were amplified on human blood leukocytes, as described previously (Holl et al., Blood, 2006, 107, 4466-4474). Virus stocks collected at peak virus production were concentrated 70-fold with a 100-kDa cutoff polyethersulfone filter (Centricon® Plus-70 Biomax Filter; MILLIPORE). Primary HIV-1 isolates were obtained from the National Institute for Biological Standards and Control (NIBSC): HIV-1_(SF162) isolate (subtype B, R5), HIV-1_(QH0) isolate (subtype B, R5 strain, R5), HIV-1_(89.6) (sub-type B, X4R5), Viruses HIV-1_(DU174) (subtype C, R5), HIV-1_(92BR025) (subtype C R5), HIV-1_(92UG024) (subtype D, X4), HIV-1_(KON) (subtype CRF02-AG, X4). HIV-1 BaL (subtype B) was provided by S. Gartner, M. Popovic, and R. Gallo (NIH).

Pseudoviruses HIV-1_(SF162) and HIV-1_(QH0) (SF162.LS and QH0692.42) were produced by co-transfection of 293T cell line with EnvC3 back bone and Envs from HIV-1_(SF162) and HIV-1_(QH0) respectively.

1.10 Neutralization Assays

Neutralization assays were performed on human PBMC and TZM-bl cells, as previously described (Mascola et al., J. Virol., 2005, 79, 10103-10107), using two standard reference strains of clade B as Env-pseudotypes viruses (SF162.LS and QH0692.42; Li et al., J. Virol., 2005, 79, 10108-10125). The 50%, 70%, 80% or 90% inhibitory dose was defined as the sample concentration that caused 50%, 70%, 80% or 90% reduction in relative luminescence units (RLU; Li et al., J. Virol., 2005, 79, 10108-10125) in TZM-bl or percentage of infected cells in PBMC, respectively.

1.11 Fc-Mediated Inhibition of HIV Replication in MDMs

Fc-mediated inhibition assay was performed on Monocyte derived macrophages (MDMs). MDMs were generated by culture of CD14+ monocytes with GM-CSF for 5 days. Inhibition of cell free HIV-1 SF162 or HIV-1 BaL replication in MDMs was assessed as previously described by Holl et al. (J. Virol., 2006, 80, 6177-6181; J. Immunol., 2004, 173, 6274-6283). Briefly, antibodies and virus were incubated for 1 h before addition to MDMs. Virus replication was measured after 48 h by the intracellular staining of p24 in MDMs by flow cytometry. Percentage of infected cells compared to control infected macrophages without antibodies was determined.

2. Results

A truncated permease antigen from M. genitalium (SEQ ID NO: 7, corresponding to amino acid sequence 431-875 of M. genitalium permease sequence SEQ ID NO: 1) was expressed in E. coli and used to immunize HAMIGA transgenic mice expressing chimeric human IgA. Groups of ten HAMIGA mice received two administrations of permease fragment in Poly I-C adjuvant via the intradermal (Group PERM/ID) and vaginal routes (Group PERM/VAG). At the same time, groups of ten HAMIGA mice were immunized with gp41-ectodomain polypeptide (SEQ ID NO: 16) (Group GP/ID; Group GP/VAG). As a negative control, five HAMIGA mice were immunized with BSA antigen (Group BSA) by ID route. IgA from vaginal washes and purified serum IgA from immunized and control HAMIGA mice were analysed.

To identify the immunization route and the antigen able to induce neutralizing immune response, neutralizing activity of seric IgA from each immunized mouse was measured against SF162 virus strain, a tier 1 isolate, in a PBMC-based neutralizing assay (FIG. 1). Although all seric IgA of PERM-immunized mice show ability to cross-react with HIV gp41 epitopes in ELISA (FIG. 2), only eight seric IgA from PERM/ID immunized mice and five seric IgA from PERM/VAG immunized mice were able to exhibit a strong potency of HIV-1 infection neutralization with an IC90 in a range of 60 μg/mL (FIG. 1). Despite a strong anti-gp41 binding (FIG. 2), no seric IgA from GP/ID and GP/VAG immunized mice groups was able to reach IC90 neutralizing activity (FIG. 1). As expected, in Bovine Serum Albumin (BSA)-immunized mice group, purified seric IgAs showed no gp41 binding by ELISA nor HIV-1 infection neutralization activity (FIG. 1).

In addition, only vaginal IgA pools from PERM/ID and PERM/VAG immunized group (n=10) exhibited a strong neutralization activity against HIV-1_(SF162) (a tier 1 isolate,) with the lowest IC90 (in a range of 1.5 to 2.5 μg/mL; Table II). Vaginal IgA pools from PERM/VAG immunized group (n=10) reached an IC50<2.5 μg/mL against QHO isolate (a tier 2 isolate) when performed in a TZM-bl cells based infection inhibition assay.

TABLE II HIV-1 specific neutralizing activity of purified vaginal IgA pools from immunized HAMIGA mice Target cells PBMC TZM Percentage of inhibition of HIV-1 infection IC90 IC50 Group of immunized HIV-1 virus HAMIGA (n = 10) SF162 QHO SF162 QHO Vaginal IgA GP/ID 0.010 >0.010 >0.01 >0.01 Vaginal IgA GP/VAG >0.016 >0.016 0.016 0.016 Vaginal IgA PERM/ID 0.0015 >0.0015 >0.0015 >0.0015 Vaginal IgA PERM/VAG 0.0025 >0.0025 0.002 0.0025 Vaginal IgA Pre-immune >0.0035 >0.0035 >0.0035 >0.0035 Vaginal IgA BSA 0.0115 >0.0115 >0.0115 >0.0115 *HIV-Infection Inhibition titers are expressed in mg/mL

The supernatants of hybridoma clones from permease-immunised mice were tested for neutralizing activity in a PBMC assay against the HIV-1_(SF162) isolate. Out of 900 hybridoma supernatants, 141 showed 80% neutralisation of the viral infection including 34 that showed 90% neutralization potency. One clone, C3G4, was sub-cloned three times and anti-permease specificities were confirmed by ELISA. One clone named C3-G4.EA5.IH2.JA11 was finally stabilized. The variable segments of the neutralizing immunoglobulin, a human chimeric IgA1,_(κ), were sequenced and analysed on IMGT data base (www.imgt.org/vquest).

TABLE III Sequence and analysis of the variable segments of the HIV-1 neutralizing human chimeric monoclonal IgA1,_(K), C3G4 Heavy chain IgH-V IgH-D IgH-J mab hIgA1 (C3G4 clone) 5-12-1*01F 1-1*01 2*01 F Mouse germline gene Identity 93.06% 82.98% AA IgHV sequence EVQMVESGGGLVKPGGSLKLSCAASGFAFNKYDMSVVVRQTPAK RLEVVVAYISGGGGHTYYRDTLKGRFTVSRDNAKNTLYLQMNSLKS EDTAMYYCTRHGTSWDYWGQGT (SEQ ID NO: 8) Light chain IgH-V IgH-J mab hIgA1 (C3G4 clone) 15-103*01 1*01 F Mouse germline gene Identity 95.34% 94.74% AA IgLV sequence DIQMNQSPSSLSASLGDTISITCRASQNINFWLSVVYQLKPGNIPKQ LIYKTSNLHTGVPSRFSGSGSGTDFTLTISSLQPEDIATYYCLQGQS YPWTFGGGTKLEIK (SEQ ID NO: 9)

The supernatant of C3G4 contains both a monomeric and polymeric monoclonal IgA1 (FIG. 3, line 1). Fractions enriched in monomeric (FIG. 3, line 2) and polymeric forms of IgA (FIG. 3, line 3) were prepared and their affinity for M. genitalium permease (FIG. 4, A) and cross-reactivity with HIV gp41 were tested in ELISA (FIG. 4, B). In each ELISA test, polymeric-IgA enriched form of C3G4 exhibited the highest affinity for M. genitalium truncated permease and gp41-ectodomain polypeptide.

Monomeric IgA and polymeric IgA enriched fractions of purified C3G4 were primarily tested in a PBMC neutralizing assay with two HIV-1 virus isolates, SF162 and QHO (FIG. 4C). Polymeric IgA enriched form strongly inhibited infection by both HIV-1 isolates SF162 (IC70 of 2 μg/mL) and QHO (IC70 of 23 μg/mL). 90% inhibition of HIV-1_(SF162) isolate infection was achieved with 126 μg/mL of polymeric IgA enriched C3G4. In each test, polymeric form of C3G4 IgA showed a greater neutralizing potency than the monomeric IgA enriched form of C3 G4.

Monomeric and polymeric forms of C3G4 were also tested in a macrophage-based neutralization assay. The assay shows the Fc-mediated inhibitory activity of the antibodies. As shown in Table IV, both forms presented 80% inhibition potency in PBMC and Macrophages-based assays, in presence of 6 μg/mL and 14 μg/mL of C3G4 IgA, respectively. Ninety percent inhibition of HIV-1 infection was achieved when both tests were performed with 58 μg/mL of C3G4 IgA polymeric form. Polymeric form of C3G4 IgA showed a greater neutralizing potency than monomeric form. The higher avidity of polymeric form may allow the antibody to recognize and capture several viral particles, as opposed to the monomeric form.

TABLE IV HIV-1 specific neutralizing activity of monomeric or polymeric enriched fractions of C3G4 IgA antibody Human cell type PBMC Macrophages HIV-1 isolate SF162 BaL HIV-1 infection inhibition titer (in mg/mL) IC80 IC90 IC80 IC90 Sam- C3G4-purified IgAl >0.125 >0.125 0.031 0.200 ples (containing two forms mix) C3G4-enriched 0.094 >0.094 0.023 0.094 monomeric IgA1 C3G4-enriched 0.006 0.058 0.014 0.058 polymeric IgA1

Neutralizing activity of monoclonal C3G4 IgA1 was also tested on different primary HIV-1 isolates (FIG. 5). Purified polymeric IgA1 exhibited a neutralization activity on nine different HIV-1 primary isolates at a low IC50 and IC80. C3G4 neutralized HIV-1_(SF162), HIV-1_(BR025) and HIV-1_(TV1) isolates with a great potency (IC80 comprised in the range of 2 to 20 μg/mL). C3G4 neutralized HIV-1_(QHO, KON, 92UG024, 89.6) and _(RW) with moderate potency (IC80>20 μg/mL).

These data demonstrate that Mycoplasma genitalium permease antigen represents a HIV-1 vaccine candidate able to prime a mucosal and systemic broadly-neutralizing protective antibody response against HIV infection in the immunized individuals.

Discussion

In this study, using HAMIGA mice to produce IgA, immunization with M. genitalium permease adjuvanted with polyI:C administered via the ID or vaginal routes elicited specific IgA Abs able to recognize the HIV-Gp41 and to neutralize HIV-1 primary isolates.

IgA is the most abundant antibody isotype produced weekly and delivered by secretion in mucosal area. Because HIV infection is usually initiated at mucosal site of entrance, the inventors assumed that IgA would better mimic the response in mucosa, including the genital mucosa. Pivotal role of polymeric form of IgA is to prevent pathogen entry by immune exclusion, but also polymeric IgA are assumed to agglutinate the virus and block transcytosis (Chomont, N. et al. Virology, 2008, 370, 246-254) and with more efficacy than their IgG homologue (Hur, E. M. et al. Blood, 2012, 120, 4571-82).

The integrity of the mucosal immune system appears to be critical for the rate of the HIV infection progression, because it is severely compromised during acute HIV infection. Beside the massive depletion of CD4+T cells, the frequency of IgA-producing B-cells in mucosal area drops dramatically, decreasing luminal secretory IgA concentrations involved in pathogens-immune exclusion protective pathway (described in both HIV and SIV infection; Alam et al., J. Viral., 2008, 82, 115-125; Muro-Cacho et al., J. Immunol., 1995, 154, 5555-5566; Douek et al., 2006, Nat. Immunol., 2006, 7, 235-239).

Transgenic mice expressing human chimeric IgA (EP patent 1 680 449) were used to ensure selection of a monoclonal IgA class antibody since a conventional immunization of wild type mice usually conduct to an IgG specific response. This mouse line was modified to express a constant human IgA heavy chain whereas constant light chain and variable genes remain from mouse origin. The C3G4-neutralizing antibody was induced by active immunization where the murine and not human repertoire has been involved in the antigen recognition. The possibility to generate the same response in human can only be evaluated in clinical trials.

Resistance to HIV infection is a rare phenomenon. Although several mechanisms may contribute including genetic factors (CCR5 d32 mutation, MHC allotype.) or immune factors such as specific IgA in vaginal secretions directed against the HIV-1 gp41, other factors may be involved.

The human and murine Ab response to many common pathogens is oligoclonal, with a restricted usage of Ig V-genes (Bos, N. A. et al., Infection and Immunity, 1996, 64, 616-623; Baxendale, H. E. & Goldblatt, D., Infection and Immunity 2006, 74, 1025-1031). In addition, in the mucosa exposed to a multitude of germs, these Abs are polyreactive and establish a natural immune homeostasis (Shimoda et al., Immunology, 1999, 97, 9-17).

Therefore, the inventors propose that the innate response to the genital tract microbiota (commensals or pathogens) could also play a role against HIV (or other pathogens) infection. The innate characteristic of the response is suggested by the oligoclonal profile of IgA found in the HEUW and the germinal feature of the Ab. The isolation of an Ab against M. genitalium cross-reacting with gp41 and neutralizing HIV-1 provides additional evidence. Whereas current thinking is that vaccine should induce hypermutated Ab in order to neutralize HIV-1 (Klein, F. et al., Cell, 2013, 153, 126-38), the inventors propose that in mucosal site, main portal of entry of the virus, non affinity matured Ab elicited by specific commensals or pathogen, could neutralize and protect against HIV infection. HEUW may have a particular unique flora with native immune response that contributes to resistance to HIV-1 infection. Comparison of the microbiota in HEUW and women who later becomes infected will help to clarify this assumption.

The key for an effective vaccine strategy seems to be the identification of the priming antigen which elicits ancestor B lineage selection and proliferation for a future maturation all along its immune history. For some viral infections, the antigen that initially activates certain naive B-cell lineages and that stimulates the memory B-cells may not be identical.

The inventors propose that this population of naive B precursors may be recruited and primed by antigens, not only from past infections but from current natural commensal micro-organisms colonization. Immunization by Mycoplasma genitalium antigens induced cross-reactive anti-HIV antibodies and elicited a systemic and mucosal broadly neutralizing anti-HIV response. IgH variable segment of one of the neutralizing monoclonal antibodies from the present study reveals a highest homology with the murine germline ancestor IgVH5-12 (FIG. 6). Interestingly, this particular murine segment shows a strong identity with the human unmutated IgVH1-2*2, ancestor of VRC01 broadly HIV neutralizing monoclonal antibody (bNab). Comparison of the IgVH regions highlights a conserved sequence covering 50 of the 98 amino acid residues, including five canonical HIV-contact residues, and particularly Arg⁷¹ _(C3G4-CRC01), which mimics the key interaction of Arg⁵⁹ _(CD4) and Asp³⁶⁸ _(gp120) (Scheid, J. F. et al., Science, 2011, 333, 1633-1637). Even if all critical residues are not conserved, the comparison of IgVH5-12 with the human IgVH1-2*2 (S18 and S19, Jardine and Schief, Science, may 2013, vol 340) suggested that the close conformational architecture of the two ancestors may be the key point of their ability to further neutralize HIV-1 infection, hIgVH1-2*2 targeting the gp120 whereas mIgVH5-12 targeting the gp41 on the surface of HIV-1 viral particles.

The inventors propose M. genitalium permease as a promising candidate to initiate a vaccine protocol mainly at the mucosal level based on its ability to prime naive B-cell clones, able to further recognize native HIV-antigens. 

1. An immunogenic composition comprising Mycoplasma sp. permease antigen or a polynucleotide encoding said antigen in expressible form in an amount effective to induce expression of HIV cross-reactive and HIV neutralizing anti-permease antibodies in a human subject following administration to the subject, and a pharmaceutically acceptable adjuvant.
 2. The immunogenic composition according to claim 1, which is a Mycoplasma genitalium permease antigen.
 3. The immunogenic composition according to claim 1, wherein said permease antigen comprises: (a) a protein comprising an amino acid sequence which is at least 85% identical to SEQ ID NO: 4, or (b) a peptide of at least 5 consecutive amino acids from said protein in (a), wherein said protein in (a) and peptide in (b) induce expression of HIV cross-reactive and HIV neutralizing anti-permease antibodies in a human subject following administration of the immunogenic composition.
 4. The immunogenic composition according to claim 3, wherein said antigen comprises a permease epitope cross-reacting with a HIV-gp41 ectodomain or C-terminal tail epitope.
 5. The immunogenic composition according to claim 4, wherein said permease epitope cross-reacts with a HIV-gp41 ectodomain epitope of SEQ ID NO:
 2. 6. The immunogenic composition according to claim 1, wherein said permease antigen comprises SEQ ID NO: 4 or
 7. 7. The immunogenic composition according to claim 1, wherein said polynucleotide comprises SEQ ID NO: 5 or
 6. 8. The immunogenic composition according to claim 1, wherein the immunogenic composition is a vaccine composition.
 9. The immunogenic composition according to claim 8, which comprises an antibody directed to said permease antigen.
 10. The immunogenic composition according to claim 9, wherein the antibody is a human or humanized IgA antibody.
 11. The immunogenic composition according to claim 1 further comprising at least one HIV antigen.
 12. A human or humanized antibody directed against M. genitalium permease, which is HIV cross-reactive and neutralizing, or a functional fragment of said antibody comprising at least the antigen-binding site.
 13. The antibody of claim 12, which is a human chimeric monoclonal IgA.
 14. The antibody of claim 13, which comprises an IgVH segment of SEQ ID NO: 8 and an IgVL segment of SEQ ID NO:
 9. 15. A method for the identification of a new vaccine candidate antigen against a pathogen of interest, comprising: (a) identifying an antigen in the mucosal microbiota of a human subject naturally resistant to said pathogen, wherein the microbiotal antigen is from a microorganism different from said pathogen, (b) generating an antibody against said microbiotal antigen in (a), (c) assaying the neutralizing activity of the antibody obtained in (b) against said pathogen, wherein a neutralizing activity of the antibody against said pathogen indicates that the microbiotal antigen is a new vaccine candidate antigen against said pathogen, for an individual susceptible to said pathogen.
 16. The immunogenic composition according to claim 2, wherein said permease antigen comprises: (a) a protein comprising an amino acid sequence which is at least 85% identical to SEQ ID NO: 4, or (b) a peptide of at least 5 consecutive amino acids from said protein in (a), wherein said protein in (a) and peptide in (b) are capable of inducing expression of HIV cross-reactive and HIV neutralizing anti-permease antibodies in a human subject following administration of the immunogenic composition.
 17. A method of inducing expression of HIV cross-reactive and HIV neutralizing anti-permease antibodies in a human subject comprising administering the immunogenic composition of claim 1 to the human subject.
 18. A method of inducing expression of HIV cross-reactive and HIV neutralizing anti-permease antibodies in a human subject comprising administering the vaccine composition of claim 8 to the human subject. 